File S1 - On the Importance of Oxidative Folding in the Evolution of Conotoxins: Cysteine Codon Preservation through Gene Duplication and Adaptation

This Supporting Information file (PDF) includes Figures S1–S11 and Tables S1–S4; it also contains a thorough discussion of the codon bias analysis methods and lists the sequences used for analysis. The rationale and methods for the codon bias analysis are presented first (including Tables S1–S4, showing sample calculations), along with the presentation of codon bias for the codons that are 4- or 6-fold redundant (Figures S1 and S2, respectively). Representative HPLC chromatograms from the folding reactions of -PVIA (Figure S3), -SIIIA (Figure S4) and -ImI (Figure S5) follow. The complete phylogenetic trees of all sequences used in the analysis are presented in Figures S6–S11, with each figure showing the tree for a single cysteine. The accession numbers of each sequence used in the analysis is also included. (PDF)